Merge dddcfdf into aa6fce9

requirements.txt

@@ -35,6 +35,7 @@ pytest-cov==2.10.1
 python-dateutil==2.8.1
 pytz==2020.1
 requests==2.24.0
+shapely==1.7.1
 scikit-learn==0.23.2
 scipy==1.5.2
 six==1.15.0

tests/test_contours.py

@@ -8,17 +8,21 @@
 import os
 
 import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.patches import Polygon
 import pandas as pd
 
-from .context import viroconcom
+from shapely.geometry import Polygon, LineString
 
 from viroconcom.params import ConstantParam, FunctionParam
 
 from viroconcom.distributions import (
     WeibullDistribution, ExponentiatedWeibullDistribution, LognormalDistribution,
     NormalDistribution, MultivariateDistribution)
 from viroconcom.contours import IFormContour, ISormContour, \
-    HighestDensityContour, DirectSamplingContour
+    HighestDensityContour, DirectSamplingContour, sort_points_to_form_continous_line
+from viroconcom.read_write import read_contour
+from viroconcom.plot import plot_contour
 
 
 _here = os.path.dirname(__file__)
@@ -720,6 +724,95 @@ def test_setup_HDC_limits_Tuple_length(self):
     #     #plt.show()
 
 
+    def test_sort_coordinates_low_n(self):
+        """
+        Sorts a limited number of points (low n).
+        """
+        # Describe a contour with correctly ordered coordinates.
+        x_correct = np.array([0, 1, 2, 3, 3, 3, 3, 2, 1])
+        y_correct = np.array([0, 0, 0, 0, 1, 2, 3, 2, 1])
+
+        # Switch two entries such that the coordinates are not ordered anymore.
+        x_us = x_correct.copy()
+        y_us = y_correct.copy()
+        x_us[3] = x_correct[6]
+        x_us[6] = x_correct[3]
+        y_us[3] = y_correct[6]
+        y_us[6] = y_correct[3]
+
+        c_sorted = sort_points_to_form_continous_line(x_us, y_us)
+        x_s = c_sorted[0]
+        y_s = c_sorted[1]
+
+        # For a manual check during development: Plot the contours.
+        fig, ax = plt.subplots()
+        plot_contour(x_correct, y_correct, ax=ax)
+        plot_contour(x_us, y_us, ax=ax, style='-r')
+        plot_contour(x_s, y_s, ax=ax, style='-g')
+        #plt.show()
+
+        np.testing.assert_array_equal(x_correct, x_s)
+        np.testing.assert_array_equal(y_correct, y_s)
+
+    def test_sort_coordinates_high_n(self):
+        """
+        Sorts an existing IFORM contour (high number of points).
+        """
+        # Load a IFORM contour that was has been computed for th EC benchmark.
+        folder_name = 'contour-coordinates/'
+        file_name_median = 'doe_john_years_25_median.txt'
+        (x_correct, y_correct) = read_contour(folder_name + file_name_median)
+
+        # Switch two entries such that the coordinates are not ordered anymore.
+        x_us = x_correct.copy()
+        y_us = y_correct.copy()
+        i1 = 10
+        i2 = 100
+        x_us[i1] = x_correct[i2]
+        x_us[i2] = x_correct[i1]
+        y_us[i1] = y_correct[i2]
+        y_us[i2] = y_correct[i1]
+        i1 = 50
+        i2 = 150
+        x_us[i1] = x_correct[i2]
+        x_us[i2] = x_correct[i1]
+        y_us[i1] = y_correct[i2]
+        y_us[i2] = y_correct[i1]
+
+        c_sorted = sort_points_to_form_continous_line(x_us, y_us)
+        x_s = c_sorted[0]
+        y_s = c_sorted[1]
+
+        # Broadly define a polygon that spans the inside of the contour.
+        coords = [(1, 1), (10, 1),
+                  (22, 7), (10, 5)]
+        poly = Polygon(coords)
+        x, y = poly.exterior.xy
+
+        # For a manual check during development: Plot the contours.
+        fig, ax = plt.subplots()
+        ax.plot(x, y)
+        plot_contour(x_correct, y_correct, ax=ax)
+        plot_contour(x_us, y_us, ax=ax, style='-r')
+        plot_contour(x_s, y_s, ax=ax, style='-g')
+        ax.plot(x_s[1], y_s[1], 'og')
+        #plt.show()
+
+        shapely_line_us = LineString(np.c_[x_us, y_us])
+        shapely_line_s = LineString(np.c_[x_s, y_s])
+
+        # Assert that the unsorted contour would cross the design region and
+        # that the sorted contour does not cross it.
+        self.assertTrue(poly.crosses(shapely_line_us))
+        self.assertFalse(poly.crosses(shapely_line_s))
+
+        # The sorting algorithm changes the direciton (clock-wise vs
+        # counter-clockwise. Thus np.testing.assert_array_equal(x_correct, x_s)
+        # would fail.
+        #np.testing.assert_array_equal(x_correct, x_s)
+        #np.testing.assert_array_equal(y_correct, y_s)
+
+
 class DirectSamplingTest(unittest.TestCase):
     def _setup(self,
                dep1=(None, None, None),

tests/test_distributions.py

@@ -1,3 +1,8 @@
+# -*- coding: utf-8 -*-
+"""
+Tests the distribution classes.
+"""
+
 import unittest
 
 

tests/test_distributions2.py

@@ -1,9 +1,13 @@
+# -*- coding: utf-8 -*-
+"""
+Tests the distribution classes.
+"""
+
 import pytest
 
 import numpy as np
 import scipy.stats as sts
 
-from .context import viroconcom
 from viroconcom.distributions import (WeibullDistribution, NormalDistribution,
                                       LognormalDistribution)
 from viroconcom.params import ConstantParam

tests/test_params.py

@@ -1,17 +1,11 @@
-#!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on Tue Sep 19 12:22:42 2017
-
-@author: nb
+Tests the parameter classes
 """
 import unittest
 
 import numpy as np
 
-
-from .context import viroconcom
-
 from viroconcom.params import ConstantParam, FunctionParam, Wrapper
 
 

tests/test_pca.py

@@ -6,8 +6,6 @@
 
 from numpy.testing import assert_allclose
 
-from .context import viroconcom
-
 from viroconcom.utility import PCA
 from viroconcom.fitting import Fit
 from viroconcom.contours import IFormContour